From 2f5755ddad550cf811f97ad6889eea2a7171a1c3 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <ricardo.wurmus@mdc-berlin.de>
Date: Fri, 16 Oct 2015 17:41:07 +0200
Subject: [PATCH] gnu: Add MOSAIK.

* gnu/packages/bioinformatics.scm (mosaik): New variable.
---
 gnu/packages/bioinformatics.scm | 46 +++++++++++++++++++++++++++++++++++++++++
 1 file changed, 46 insertions(+)

diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 069e52f..e339a70 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -2248,6 +2248,52 @@ viewer.")
                                    (string-append bin "/samtools")))))
            (delete 'patch-tests)))))))
 
+(define-public mosaik
+  (let ((commit "5c25216d"))
+    (package
+      (name "mosaik")
+      (version "2.2.30")
+      (source (origin
+                ;; There are no release tarballs nor tags.
+                (method git-fetch)
+                (uri (git-reference
+                      (url "https://github.com/wanpinglee/MOSAIK.git")
+                      (commit commit)))
+                (file-name (string-append name "-" version))
+                (sha256
+                 (base32
+                  "17gj3s07cm77r41z92awh0bim7w7q7fbn0sf5nkqmcm1vw052qgw"))))
+      (build-system gnu-build-system)
+      (arguments
+       `(#:tests? #f ; no tests
+         #:make-flags (list "CC=gcc")
+         #:phases
+         (modify-phases %standard-phases
+           (replace 'configure
+                    (lambda _ (chdir "src") #t))
+           (replace 'install
+                    (lambda* (#:key outputs #:allow-other-keys)
+                      (let ((bin (string-append (assoc-ref outputs "out")
+                                                "/bin")))
+                        (mkdir-p bin)
+                        (copy-recursively "../bin" bin)
+                        #t))))))
+      (inputs
+       `(("perl" ,perl)
+         ("zlib" ,zlib)))
+      (home-page "https://code.google.com/p/mosaik-aligner/")
+      (synopsis "Map nucleotide sequence reads to reference genomes")
+      (description
+       "MOSAIK is a program for mapping second and third-generation sequencing
+reads to a reference genome.  MOSAIK can align reads generated by all the
+major sequencing technologies, including Illumina, Applied Biosystems SOLiD,
+Roche 454, Ion Torrent and Pacific BioSciences SMRT.")
+      ;; MOSAIK is released under the GPLv2+ with the exception of third-party
+      ;; code released into the public domain:
+      ;; 1. fastlz by Ariya Hidayat - http://www.fastlz.org/
+      ;; 2. MD5 implementation - RSA Data Security, RFC 1321
+      (license (list license:gpl2+ license:public-domain)))))
+
 (define-public ngs-sdk
   (package
     (name "ngs-sdk")
-- 
2.1.0